Variant report

Variant	rs9969657
Chromosome Location	chr8:10515278-10515279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10096777	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11250056	0.86[EUR][1000 genomes]
rs11774552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781592	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28459259	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28680211	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28722737	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4368940	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4395858	0.92[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4841407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4841409	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4841411	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56057779	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7814795	0.96[CEU][hapmap];0.94[CHD][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9969466	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030934	chr8:10065169-10561161	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1025557	chr8:10216726-10555187	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv610267	chr8:10268736-10526742	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1015932	chr8:10357101-10597856	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1021048	chr8:10504395-10591896	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9969657	DEFB136	cis	parietal	SCAN
rs9969657	CTSB	cis	cerebellum	SCAN
rs9969657	TDH	cis	cerebellum	SCAN
rs9969657	CLDN23	cis	multi-tissue	Pritchard
rs9969657	TDH	cis	parietal	SCAN
rs9969657	FLJ10661	cis	cerebellum	SCAN
rs9969657	PRSS55	cis	cerebellum	SCAN
rs9969657	FAM167A	cis	lymphoblastoid	seeQTL
rs9969657	C8orf13	cis	multi-tissue	Pritchard
rs9969657	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10512600-10519000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:10513000-10522800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:10513000-10524200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:10513600-10519200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:10513800-10516800	Weak transcription	Adipose Nuclei	Adipose
6	chr8:10514600-10515600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links